User:Ab2111

Current projects

Torsional movesets for biomolecules: Biased Gaussian Sampling

Favrin et. al have developed a movecass for MC simulations of biomolecules: Biased Gaussian Sampling (BGS) refers to a perturbation moveset on a contiguous set of $n\geq 8$ backbone torsional angles. During a trial move, each of the $n$ torsions is perturbed randomly, but in a way that biases towards a local deformation. The vector of torsional perturbations ${\delta {\vec {\psi }}=(\delta \psi _{1},\cdots ,\delta \psi _{n})}$ samples the distribution $P(\delta {\vec {\psi }})\propto \exp \left[-{\frac {a}{2}}{\delta {\vec {\psi }}}^{T}({\mathbf {1} }+b{\mathbf {G} }){\delta {\vec {\psi }}}\right]$, where ${\mathbf {G} }$ is a conformation-dependent $n\times n$ matrix that biases towards local deformations. The constants $a$ and $b$ control the size of the average perturbation, and the bias towards local deformation, respectively.

Regime of utility

The authors developed BGS for canonical ensemble (constant NVT) simulations using Monte Carlo dynamics, and note that the method can perform significantly better than standard pivot moves (perturbation of a single backbone torsion), especially at low temperatures. Because the bias towards local deformations acts to localize the MC perturbations to a specific region of the protein, the BGS moves can prevent unexpected steric clashes between many atoms which lead to large changes of energy. While at low temperatures BGS can be very effective, the authors state that at higher temperatures it doesn't perform much better than standard pivot moves.

I have not yet benchmarked BGS with Basin-Hopping, although I could imagine it could be very useful in probing secondary structure (alpha helicity, beta sheets), as it has for NVT simulations. However, the bias towards local deformations may not be as crucial since we are always minimizing.

Implementation in GMIN

The BGS moveset is currently implemented as a part of a larger DIHEDRALROTATION move.

BGSMOVE a b pselectBGS [NDIHEDRAL_BB_GROUPS]

$a,b$: BGS parameters described above pselectBGS : probability of attempting BGS move (if not selected, a standard DIHEDRALROTATION move is attempted) NDIHEDRAL_BB_GROUPS : number of backbone groups in dihedralgroups file, defaults to NDIHEDRALGROUPS

Dependencies: DIHEDRALROTATION keyword must be present